Fathead minnows are very hard to see in a pond, at least mine are! The rosy red minnows which are just an orange variant of the same species are much easier to see in the pond. It's a good idea to quarantine fatheads from a bait shop (or those sold as "feeders") as they are usually in poor health.
Which species of shiner did the bait shop have? There are many kinds. Some species stay just a few inches long like red shiners. Others grow larger.
In a new pond, especially one without a lot of other animals and plant cover, fatheads will hide a lot. That's normal. Once they settle in, they will be more adventurous. My minnows zip to the top and eat their flakes like little piggies but it took them the first season to get over their fear. I think you got enough minnows (assuming no more have died). I don't suggest getting the shiners until you find out which species that they are.
As you said, white cloud mountain minnows are not able to overwinter (although I've had a few people tell me that they can). They are native to China. It is good that you want to have a native fish pond. My page on native fish is at
http://www.fishpondinfo.com/misc2.htmGood luck!